NTFS does not support linux file permissions, so it wouldn't work anyway unless you symlinked each individual folder. Valve has also said that symlinking to an NTFS partition will likely corrupt your gcfs and you should not do it.

I fixed the permission denied issue by specifying dmask=022,fmask=023 when mounting the NTFS partition. But now I get a similar crash to the desktop as dymoblade describes right before the valve video is shown. Neither -nojoy or disabling the in-game steam community helped. Here is the log:

Game update: AppID 520 "Team Fortress 2 Beta", ProcID 8991, IP 0.0.0.0:0saving roaming config store to 'sharedconfig.vdf'roaming config store 2 saved successfullySDL video target is 'x11'SDL video target is 'x11'SDL failed to create GL compatibility profile (whichProfile=0!This system supports the OpenGL extension GL_EXT_framebuffer_object.This system supports the OpenGL extension GL_EXT_framebuffer_blit.This system supports the OpenGL extension GL_EXT_framebuffer_multisample.This system DOES NOT support the OpenGL extension GL_APPLE_fence.This system supports the OpenGL extension GL_NV_fence.This system supports the OpenGL extension GL_ARB_sync.This system supports the OpenGL extension GL_EXT_draw_buffers2.This system supports the OpenGL extension GL_EXT_bindable_uniform.This system DOES NOT support the OpenGL extension GL_APPLE_flush_buffer_range.This system supports the OpenGL extension GL_ARB_map_buffer_range.This system supports the OpenGL extension GL_ARB_vertex_buffer_object.This system supports the OpenGL extension GL_ARB_occlusion_query.This system DOES NOT support the OpenGL extension GL_APPLE_texture_range.This system DOES NOT support the OpenGL extension GL_APPLE_client_storage.This system DOES NOT support the OpenGL extension GL_ARB_uniform_buffer.This system supports the OpenGL extension GL_ARB_vertex_array_bgra.This system supports the OpenGL extension GL_EXT_vertex_array_bgra.This system supports the OpenGL extension GL_ARB_framebuffer_object.This system DOES NOT support the OpenGL extension GL_GREMEDY_string_marker.This system supports the OpenGL extension GL_ARB_debug_output.This system supports the OpenGL extension GL_EXT_direct_state_access.This system DOES NOT support the OpenGL extension GL_NV_bindless_texture.This system DOES NOT support the OpenGL extension GL_AMD_pinned_memory.This system supports the OpenGL extension GL_EXT_framebuffer_multisample_blit_scaled.This system supports the OpenGL extension GL_EXT_texture_sRGB_decode.This system supports the OpenGL extension GL_NVX_gpu_memory_info.This system DOES NOT support the OpenGL extension GL_ATI_meminfo.This system supports the OpenGL extension GL_EXT_texture_compression_s3tc.This system supports the OpenGL extension GLX_EXT_swap_control_tear.GL_NV_bindless_texture: DISABLEDGL_AMD_pinned_memory: DISABLEDGL_EXT_texture_sRGB_decode: AVAILABLEUsing breakpad crash handlerSetting breakpad minidump AppID = 520Forcing breakpad minidump interfaces to loadLooking up breakpad interfaces from steamclientCalling BreakpadMiniDumpSystemInitInstalling breakpad exception handler for appid(520)/version(5140_client)Looking up breakpad interfaces from steamclientCalling BreakpadMiniDumpSystemInitSteam_SetMinidumpSteamID: Caching Steam ID: XXXX [API loaded yes]Steam_SetMinidumpSteamID: Setting Steam ID: XXXXConVarRef m_rawinput doesn't point to an existing ConVarGL_NVX_gpu_memory_info: AVAILABLEGL_ATI_meminfo: UNAVAILABLEGL_NVX_gpu_memory_info: Total Dedicated: 1047872, Total Avail: 1048576, Current Avail: 799496GL_MAX_SAMPLES_EXT: 32Could not load chromehtml library.IDirect3DDevice9::Create: BackBufWidth: 1920, BackBufHeight: 1200, D3DFMT: 3, BackBufCount: 1, MultisampleType: 0, MultisampleQuality: 0Error: Material "fullscreenvideomaterial" uses unknown shader "Bik"Uploading dump (in-process) [proxy '']/tmp/dumps/crash_20121219164606_1.dmpsuccess = yesresponse: CrashID=bp-3dea4ebf-37a0-47fd-951a-2ba472121219/home/__USER__/.local/share/Steam/SteamApps/__STEAM_USER__/Team Fortress 2 Beta/hl2.sh: line 72: 8998 Segmentation fault (core dumped) ${GAME_DEBUGGER} "${GAMEROOT}"/${GAMEEXE} "$@"Game removed: AppID 520 "Team Fortress 2 Beta", ProcID 8998